2DTN | pdb_00002dtn

Crystal structure of Helicobacter pylori undecaprenyl pyrophosphate synthase complexed with pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb2DTN/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-07-13 Released: 2007-06-26 
• Deposition Author(s): Guo, R.T., Kuo, C.J., Chen, C.L., Ko, T.P., Liang, P.H., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.293 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.215 (DCC) 

Starting Model: experimental

Literature

Biochemical characterization, crystal structure, and inhibitors of Helicobacter pylori undecaprenyl pyrophosphate synthase

Kuo, C.J., Guo, R.T., Lu, I.L., Liu, H.G., Wu, S.Y., Ko, T.P., Wang, A.H.-J., Liang, P.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.33 kDa 
• Atom Count: 3,582 
• Modeled Residue Count: 417 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
undecaprenyl pyrophosphate synthase	A, B	245	Helicobacter pylori	Mutation(s): 0  EC: 2.5.1.31 (PDB Primary Data), 2.5.1 (UniProt)
UniProt
Find proteins for P55984 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P55984  Go to UniProtKB:  P55984

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPO	C [auth B]	DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.293 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.215 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.431	α = 90
b = 58.763	β = 90
c = 154.185	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Guo, R.T., Kuo, C.J., Chen, C.L., Ko, T.P., Liang, P.H., Wang, A.H.-J.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description